Package eu.isas.peptideshaker.recalibration

Class SpectrumRecalibrator

java.lang.Object
eu.isas.peptideshaker.recalibration.SpectrumRecalibrator
public class SpectrumRecalibrator extends Object
This class recalibrates spectra.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    SpectrumRecalibrator()
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    clearErrors(String spectrumFileName)
    Clears the loaded error statistics for the given file name in order to save memory.
    void
    estimateErrors(String spectrumFileNameWithoutExtension, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Estimates the file m/z errors and displays the progress in a waiting handler.
    RunMzDeviation
    getRunMzDeviations(String spectrumFileName)
    Returns the mz deviation statistics class for the spectrum file of interest.
    com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum
    recalibrateSpectrum(String fileName, String spectrumTitle, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, boolean recalibratePrecursor, boolean recalibrateFragmentIons)
    Recalibrates a spectrum.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • SpectrumRecalibrator

      public SpectrumRecalibrator()
      Constructor.

  • Method Details

    • clearErrors

      public void clearErrors(String spectrumFileName)
      Clears the loaded error statistics for the given file name in order to save memory.
      Parameters:
      spectrumFileName - the spectrum file name

    • getRunMzDeviations

      public RunMzDeviation getRunMzDeviations(String spectrumFileName)
      Returns the mz deviation statistics class for the spectrum file of interest. Null if not estimated.
      Parameters:
      spectrumFileName - name of the spectrum file
      Returns:
      the mz deviation statistics

    • estimateErrors

      public void estimateErrors(String spectrumFileNameWithoutExtension, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Estimates the file m/z errors and displays the progress in a waiting handler. Shall be done before calibration. The information generated can be cleared from the mapping using clearErrors(String spectrumFileName). The progress will only be updated, max value is the number of spectra
      Parameters:
      spectrumFileNameWithoutExtension - the name of the file of the run
      identification - the corresponding identification
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      identificationParameters - the identification parameters
      waitingHandler - a waiting handler displaying the progress and allowing the user to cancel the process. Can be null

    • recalibrateSpectrum

      public com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum recalibrateSpectrum(String fileName, String spectrumTitle, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, boolean recalibratePrecursor, boolean recalibrateFragmentIons)
      Recalibrates a spectrum.
      Parameters:
      fileName - the name of the file where to find the spectrum
      spectrumTitle - the title of the spectrum
      spectrumProvider - the spectrum provider
      recalibratePrecursor - boolean indicating whether precursors shall be recalibrated
      recalibrateFragmentIons - boolean indicating whether fragment ions shall be recalibrated
      Returns:
      a recalibrated spectrum